General information for g5594.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable cysteine–tRNA ligase, mitochondrial.
Parent gene
- The parent gene g5594 is located on chr_2: 10446699..10448950 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_2 | g5594 | g5594.t1 | isoform | g5594.t1 | 10445111 | 10446699 |
| chr_2 | g5594 | g5594.t1 | exon | g5594.t1.exon1 | 10445111 | 10445268 |
| chr_2 | g5594 | g5594.t1 | cds | g5594.t1.CDS1 | 10445111 | 10445268 |
| chr_2 | g5594 | g5594.t1 | exon | g5594.t1.exon2 | 10445334 | 10446699 |
| chr_2 | g5594 | g5594.t1 | cds | g5594.t1.CDS2 | 10445334 | 10446699 |
| chr_2 | g5594 | g5594.t1 | TTS | g5594.t1 | 10446724 | 10446724 |
| chr_2 | g5594 | g5594.t1 | TSS | g5594.t1 | NA | NA |
Sequences
>g5594.t1 Gene=g5594 Length=1524
ATGTCGTTATTAAGAAGAGTAAATTTTAATTTAAGCCGTCTTTCAAAAAGAACAAATTGT
CATGGAATAAAAACTGATATAAATATTTATAGTTATCGAGACAAGCGCAAAGTGCCATTA
GTTTTAGCAAATCCTATTTATTCATCCTGGTACACTTGTGGTCCAACAGTTTATGATTCT
GCTCACATTGGTCATGGTTCAACATATGTTCGACTTGATATCATTCAACGCATTCTTAGA
AATTATTTTAATATCAACTTAGTAACATGCATGAACATCACAAATATCGATGATAAAATT
ATAAAAAGAAGTAATGAATTAGGAAAAGATTGGAATTTATTAGCAGAAGAATATGAAATT
GAATTTTGGGATGATTTAAATAAATTGAATATCATGCAACCAGATATAAAACTAAGAGTG
ACTGATAAAATCCCAGAAATAATTAAATTCATAGAAGAAATTGAAAAGAAAGGATATACA
ACTATCTCAACAAATGGATCAGTGAATTTCAAAACTTCTGCCTACAGTAAATATGGAAAA
CTGCATAATGTCGTTCTTGAAGATGTTTCAACAGCAGAATTTGCTCTTTGGAAGGCAGCA
AAAGAGAACGAACCTTGGTGGGATTCAAAATGGGGAAGAGGAAGACCAGGATGGCATATC
GAGTGTTCAACATTAGCAAGTCTTGTTTTTGGTTCACATTTAGATTTTCATGCAGGTGGA
ATTGATTTGAAATTTCCACATCATGAAAATGAAGAAGCACAAAGCTGCGTGTTTCATAAT
TGTAACGATTGGGTTCAAAATTGGATACATACTGGACATTTACATTTAAAAGGACAAAGT
GAAAAGATGTCAAAATCACTTAAAAATACAATTTCAATAAGAGATTTTTTGAAAGATTAT
ACAGCAGAAAAATTTCGAATGGCATGCTTATTATCACATTATCGTTCATCAATTGAGTTT
GGTCCAGAATTAATGTTTGCTGCTGATTCTATTCTCAAACGGGTCAAATCATTTAAAGAA
GACGTTAAAGCATTTATTAGTGGTGCAAAAATTGATGGATATGTCAATGAAGAAGAATTG
AGAAAACATTTTCAAGAATCTAGAAATAATATTGATGAAGCTCTAAGAGATGATTTTCAT
ACTGCTGCATGCATTGGTCAATTATCTGATTTGATGCGACTTATAAGTAAAACAATAAAT
AATGTGGATAAAAAAAATGAACAGAGGTCATCAAATGGAAATGAAAAAGCGCTTTTATAT
GCTGTAGTAAATTATATTGATCACATGCTACAAATTTTTGGAATTGGCGATGAAATTCAA
TTTAGTGAATCATATGATGAGGGTCGAATGGAAAATTTAGTTAATTCGATTATAAAAGTT
AGAAATGACATTCGATTAAGAGCTAAAGAAACTAAAAGTAAAGAGCTATTTCAAGTGTGC
GATGAAATAAGGCAATCAATGAGAGAGAATTTAATAGAAATCAAAGACCATGGAAATTTA
TCGTCATGGAGTAAAGTAAAATAA
>g5594.t1 Gene=g5594 Length=507
MSLLRRVNFNLSRLSKRTNCHGIKTDINIYSYRDKRKVPLVLANPIYSSWYTCGPTVYDS
AHIGHGSTYVRLDIIQRILRNYFNINLVTCMNITNIDDKIIKRSNELGKDWNLLAEEYEI
EFWDDLNKLNIMQPDIKLRVTDKIPEIIKFIEEIEKKGYTTISTNGSVNFKTSAYSKYGK
LHNVVLEDVSTAEFALWKAAKENEPWWDSKWGRGRPGWHIECSTLASLVFGSHLDFHAGG
IDLKFPHHENEEAQSCVFHNCNDWVQNWIHTGHLHLKGQSEKMSKSLKNTISIRDFLKDY
TAEKFRMACLLSHYRSSIEFGPELMFAADSILKRVKSFKEDVKAFISGAKIDGYVNEEEL
RKHFQESRNNIDEALRDDFHTAACIGQLSDLMRLISKTINNVDKKNEQRSSNGNEKALLY
AVVNYIDHMLQIFGIGDEIQFSESYDEGRMENLVNSIIKVRNDIRLRAKETKSKELFQVC
DEIRQSMRENLIEIKDHGNLSSWSKVK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g5594.t1 | CDD | cd00672 | CysRS_core | 28 | 320 | 7.07242E-91 |
| 13 | g5594.t1 | Coils | Coil | Coil | 357 | 377 | - |
| 11 | g5594.t1 | Gene3D | G3DSA:3.40.50.620 | HUPs | 10 | 321 | 6.0E-106 |
| 12 | g5594.t1 | Gene3D | G3DSA:1.20.120.640 | - | 325 | 505 | 1.7E-11 |
| 4 | g5594.t1 | Hamap | MF_00041 | Cysteine–tRNA ligase [cysS]. | 27 | 506 | 27.324989 |
| 2 | g5594.t1 | PANTHER | PTHR10890:SF27 | CYSTEINE–TRNA LIGASE, MITOCHONDRIAL-RELATED | 21 | 504 | 8.6E-173 |
| 3 | g5594.t1 | PANTHER | PTHR10890 | CYSTEINYL-TRNA SYNTHETASE | 21 | 504 | 8.6E-173 |
| 7 | g5594.t1 | PRINTS | PR00983 | Cysteinyl-tRNA synthetase signature | 50 | 61 | 7.4E-24 |
| 8 | g5594.t1 | PRINTS | PR00983 | Cysteinyl-tRNA synthetase signature | 87 | 96 | 7.4E-24 |
| 6 | g5594.t1 | PRINTS | PR00983 | Cysteinyl-tRNA synthetase signature | 204 | 222 | 7.4E-24 |
| 5 | g5594.t1 | PRINTS | PR00983 | Cysteinyl-tRNA synthetase signature | 235 | 256 | 7.4E-24 |
| 1 | g5594.t1 | Pfam | PF01406 | tRNA synthetases class I (C) catalytic domain | 49 | 327 | 1.9E-96 |
| 9 | g5594.t1 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 27 | 327 | 1.37E-68 |
| 10 | g5594.t1 | SUPERFAMILY | SSF47323 | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 356 | 504 | 4.45E-15 |
| 15 | g5594.t1 | TIGRFAM | TIGR00435 | cysS: cysteine–tRNA ligase | 28 | 505 | 3.2E-118 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5594/g5594.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5594.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004817 | cysteine-tRNA ligase activity | MF |
| GO:0006423 | cysteinyl-tRNA aminoacylation | BP |
| GO:0005524 | ATP binding | MF |
| GO:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01883 (cysteinyl-tRNA synthetase)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
